After the Mexican War, John Brannan fought the Seminoles in various posts.
When the Civil War came, he was appointed brigadier general of volunteers and placed in command of the Department of Key West. In October 1862 he fought at the Battle of Saint John's Bluff on the St. John's River for control of the Jacksonville, Florida.
In 1863, he led an infantry division during the Tullahoma Campaign. He was with General George Thomas at Chickamauga, where his division lost 38% of its troops.
From October 1863 to June 1865, he was chief of artillery for the Department of Cumberland where he oversaw the defenses of Chattanooga.
He was at the Battle of Missionary Ridge and the Atlanta Campaign.
From July 10 to September 25, 1865, he commanded the Department of Savannah.